Scattered throughout the continent are mystery dungeons, labyrinth-like structures with several floors that the player must traverse to complete missions. They are home to many hostile Pokémon, although some Pokémon are not as hostile, such as Kecleon and the Pokémon in the Secret Bazaar. They change their layout every time they are entered, making it impossible to predict how to get through beforehand.

There are apparently very few humans in this Pokémon world, and they are often discussed or referenced throughout the game. The in-game description of the Friend Area "Decrepit Lab" claims that this specific Friend Area was built by humans long ago. As referenced by the Generation IV Mystery Dungeon games, a few humans do live in this world acting as they do in the mainstream Pokémon games. It was referenced by Grovyle who said that the player was their human partner; shocking the player's partner who never would have thought of the idea.

The geography of the maps of this world is similar between the Generation III games and the Generation IV games, although it is not established that they are the same world. All three Pokémon Mystery Dungeon for WiiWare games do not have a world map.